Is there a niche for DNA microarrays in molecular diagnostics?

Expert Review of Molecular Diagnostics

Volumn 10, Issue 7, 2010, Pages 875-882

  Jordan, Bertrand R ^a  

^a Parc Scientifique de Luminy   (France)

Author keywords

clinical utility; diagnostics; DNA arrays; expression; prediction; prognostic; regulation

Indexed keywords

DIAGNOSTIC ACCURACY; DNA MICROARRAY; GENE EXPRESSION; GENE SEQUENCE; GENOTYPE; HUMAN; MOLECULAR DIAGNOSIS; POLYMERASE CHAIN REACTION; REVIEW; ARTICLE; GENE EXPRESSION PROFILING; HUMAN GENOME; METHODOLOGY; MOLECULAR PATHOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

GENE EXPRESSION PROFILING; GENOME, HUMAN; GENOTYPE; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATHOLOGY, MOLECULAR; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 79952200833     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/erm.10.74     Document Type: Review

References (33)

1. Ashley EA, Butte AJ, Wheeler MT et al. Clinical assessment incorporating a personal genome. Lancet 375, 1525-1535 (2010).
2. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470 (1995).
3. Jain KK. Applications of AmpliChip CYP450. Mol. Diagn. 9, 119-127 (2005).
4. Glas AM, Floore A, Delahaye LJ et al. Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics 7, 278 (2006).
5. Li X, Quigg RJ, Zhou J, Gu W, Nagesh Rao P, Reed EF. Clinical utility of microarrays: current status, existing challenges and future outlook. Curr. Genomics 9(7), 466-474 (2008).
6. Tezak Z, Ranamukhaarachchi D, Russek-Cohen E, Gutman S. FDA perspectives on potential microarray-based clinical diagnostics. Hum. Genomics 2, 236-243 (2006). (Pubitemid 43192226)
7. Leinonen M, Nieminen P, Kotaniemi-Talonen L et al. Age-specific evaluation of primary human papillomavirus screening vs conventional cytology in a randomized setting. J. Natl Cancer Inst. 101(23), 1612-1623 (2009).
8. Watson MS, Cutting GR, Desnick RJ et al. Cystic fibrosis population carrier screening: 2004. revision of American College of Medical Genetics mutation panel. Genet. Med. 6, 387-391 (2004). (Pubitemid 39310514)
9. Daly AK. Pharmacogenetics of the major polymorphic metabolizing enzymes. Fundam. Clin. Pharmacol. 17, 27-41 (2003). (Pubitemid 36241451)
10. Katsanis SH, Javitt G, Hudso K. A case study of personalized medicine. Science 320, 53-54 (2008).
11. Veltman JA. Genomic microarrays in clinical diagnosis. Curr. Opin. Pediatr. 18, 598-603 (2006). (Pubitemid 44747151)
12. Bejjani BA, Shaffer LG. Application of array-based comparative genomic hybridization to clinical diagnostics. J. Mol. Diagn. 8, 528-553 (2006).
13. Reich DE, Lander ES. On the allelic spectrum of human disease. Trends Genet. 17, 502-510 (2001). (Pubitemid 32763048)
14. Manolio TA, Collins FS, Cox NJ et al. Finding the missing heritability of complex diseases. Nature 461, 747-753 (2009).
15. Campbell G. Some issues in the statistical evaluation of genetic and genomic tests. J. Biopharm. Stat. 14, 539-552 (2004). (Pubitemid 39296085)
16. Quackenbush J. Microarray analysis and tumor classification. N. Engl. J. Med. 354(23), 2463-2472 (2006). (Pubitemid 43855049)
17. Ein-Dor L, Zuk O, Domany E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc. Natl Acad. Sci. USA 103(15), 5923-5928 (2006).
18. van de Vijver MJ, He YD, van't Veer LJ et al. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 347(25), 1999-2009 (2002). (Pubitemid 35461656)
19. Buyse M, Loi S, van't Veer L et al. Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J. Natl Cancer Inst. 98, 1183-1192 (2006). (Pubitemid 44390989)
20. Paik S, Shak S, Tang G et al. A multigene assay to predict recurrence of tamoxifentreated, node-negative breast cancer. N. Engl. J. Med. 351(27), 2817-2826 (2004). (Pubitemid 40051905)
21. Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group. Recommendations from the EGAPP Working Group: can tumor gene expression profiling improve outcomes in patients with breast cancer? Genet. Med. 11(1), 66-73 (2009).
22. Koscielny S. Why most gene expression signatures of tumors have not been useful in the clinic. Sci. Transl. Med. 2(14), 14ps2 (2010).
23. Cardoso F, Piccart-Gebhart M, van't Veer L, Rutgers E; TRANSBIG Consortium. The MINDACT trial: the first prospective clinical validation of a genomic tool. Mol. Oncol. 1(3), 246-251 (2007). (Pubitemid 350181650)
24. Mook S, van't Veer LJ, Rutgers EJ, Piccart-Gebhart MJ, Cardoso F. Individualization of therapy using Mammaprint: from development to the MINDACT Trial. Cancer Genomics Proteomics 4(3), 147-155 (2007).
25. Zujewski JA, Kamin L. Trial assessing individualized options for treatment for breast cancer: the TAILORx trial. Future Oncol. 4(5), 603-610 (2008).
26. Ross JS, Hatzis C, Symmans WF, Pusztai L, Hortobágyi GN. Commercialized multigene predictors of clinical outcome for breast cancer. Oncologist 13, 477-493 (2008). (Pubitemid 351872866)
27. Dumur CI, Lyons-Weiler M, Sciulli C, et al. Interlaboratory performance of a microarray-based gene expression test to determine tissue of origin in poorly differentiated and undifferentiated cancers. J. Mol. Diagn. 10, 67-77 (2008). (Pubitemid 351184837)
28. Sotiriou C, Wirapati P, Loi S et al. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J. Natl Cancer Inst. 98(4), 262-272 (2006). (Pubitemid 43264710)
29. Valk PJ, Verhaak RG, Beijen MA et al. Prognostically useful gene-expression profiles in acute myeloid leukemia. N. Engl. J. Med. 350(16), 1617-1628 (2004). (Pubitemid 38528701)
30. Spira A, Beane JE, Shah V et al. Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer. Nat. Med. 13(3), 361-366 (2007). (Pubitemid 46376687)
31. Negrini M, Nicoloso MS, Calin GA. MicroRNAs and cancer-new paradigms in molecular oncology. Curr. Opin. Cell Biol. 21(3), 470-479 (2009).
32. Metzker ML. Sequencing technologies-the next generation. Nat. Rev. Genet. 11(1), 31-46 (2010).
33. Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annu. Rev. Genomics Hum. Genet. 10, 135-151 (2009).